Contacts of the helix formed by residues 187 - 193 (chain B) in PDB entry 1ESQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186B GLY* 1.3 76.5 + - - +
188B LYS* 1.3 74.6 + - + +
189B LEU* 3.1 50.8 + - + +
190B LEU* 3.2 23.3 + - - +
229B ALA* 4.2 11.4 - - + +
230B GLN* 4.5 3.8 - - + +
233B ALA* 3.5 30.3 - - + +
244B PHE* 4.9 2.7 - - + -
305B ATP 3.4 18.3 + - - -
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Residues in contact with LYS 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B HIS* 1.3 85.1 + - + +
189B LEU* 1.3 57.3 + - - +
191B THR* 2.9 38.6 + - - +
192B LYS* 4.7 2.8 - - + +
305B ATP 3.6 29.3 + - - +
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Residues in contact with LEU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B HIS* 3.1 28.2 - - + +
188B LYS* 1.3 71.6 - - - +
190B LEU* 1.3 53.0 + - - +
191B THR 2.9 5.6 - - - -
192B LYS* 2.7 43.8 + - + +
193B VAL* 3.4 8.7 + - - +
233B ALA* 4.4 5.6 - - + +
236B THR* 4.4 12.8 - - + -
237B ALA 4.6 9.9 - - - +
240B GLY* 4.9 2.2 - - - -
241B PRO* 4.7 22.9 - - + -
244B PHE* 3.4 43.1 - - + -
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Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B GLY* 4.3 0.7 - - - -
187B HIS 3.2 19.9 + - - +
188B LYS 3.1 0.6 - - - -
189B LEU* 1.3 76.8 - - - +
191B THR* 1.3 59.4 + - - +
192B LYS 3.2 1.0 + - - -
193B VAL* 3.3 11.2 + - + +
196B ALA* 3.3 32.2 - - + +
225B TYR* 4.1 24.0 - - + +
229B ALA* 3.6 24.7 - - + -
244B PHE* 3.5 25.0 - - + -
248B LEU* 4.4 10.3 - - + -
305B ATP 3.1 46.0 - - - +
360B MG 4.2 3.1 - - - -
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Residues in contact with THR 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B LYS* 2.9 24.6 + - + +
189B LEU 2.9 0.4 - - - -
190B LEU* 1.3 80.2 - - - +
192B LYS* 1.3 64.5 + - + +
193B VAL 3.5 0.6 + - - +
305B ATP 3.9 33.2 + - - +
360B MG 4.5 8.3 - - - -
37C LEU* 4.3 15.1 - - - +
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Residues in contact with LYS 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B LYS* 4.7 2.7 - - + +
189B LEU* 2.7 26.5 + - + +
191B THR* 1.3 90.5 - - + +
193B VAL* 1.3 60.9 + - - +
194B THR 3.9 0.2 + - - -
241B PRO* 3.9 37.8 - - + +
34C ASN* 4.0 6.2 + - - +
37C LEU* 2.9 51.5 + - + +
38C ALA 3.3 13.9 + - - -
39C LEU 4.9 0.2 - - - -
40C GLY* 4.5 6.9 - - - +
253C SER* 4.3 5.3 - - - -
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Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B PHE* 4.0 21.5 - - + -
189B LEU 3.7 3.4 - - - +
190B LEU* 3.3 10.1 + - + +
191B THR 5.2 0.2 - - - -
192B LYS* 1.3 82.7 - - + +
194B THR* 1.3 73.5 + - - +
196B ALA* 3.1 24.2 + - + +
241B PRO 4.0 15.7 - - - +
244B PHE* 3.6 32.3 - - + -
245B GLN* 4.0 24.2 - - + +
248B LEU* 6.5 0.2 - - + -
325B TZP 4.4 1.6 + - - -
34C ASN* 3.7 8.7 - - - +
37C LEU* 4.1 1.8 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il